I use tmdb episode ordering for this show and they match correctly once you name the files correctly. The Heart of Archness episodes are considered specials, see the link for details → Archer: Season 0 — The Movie Database (TMDB)
So, Archer - S00E03, Archer - S00E04 and Archer - S00E05 would be how you name those episodes.
Looking at tvdb does the same Archer (2009) - Aired Order - Specials - TheTVDB.com
You may need to plex dance the show if you have manually done edits.
